Posts by JCVI Staff

The JCVI family mourns the loss of a true friend and generous supporter, Dr. J. Robert Beyster. Dr. Beyster was a World War II Veteran, a nuclear engineer whose research propelled the Department of Defense’s weapons systems and submarines into the future of war fighting, but most notably, he founded Science Applications International Corporation (SAIC), an employee-owned multi-billion dollar corporation.

Bob and Betty Beyster

The Beyster Family have been generous supporters of science programs at the JCVI since 2009 when they, along with matching funds from Life Technologies Foundation, sponsored a two year leg of the Sorcerer II Global Ocean Sampling Expedition. This substantial support from the Beyster Family enabled sampling research of microbial life in the waters of the Baltic, Mediterranean, and Black Seas. These are scientifically important because they are among the world’s largest seas isolated from the major oceans. To date more than 80 million new genes and protein families have been discovered as part of the Sorcerer II Expedition.

The Beysters have also supported JCVI scientist Andy Allen, Ph.D. and his Southern California Upwelling Sampling Project. Dr. Allen has conducted sampling expeditions along the Southern California coast to better understand the microbes living in these waters. Dr. Beyster participated in 8 of the 11 sampling excursions that were conducted from his own boat, Solutions. He blogged about a major regional dinoflagellate bloom that was sampled as part of this project.

Importantly, this work has led to an exciting new San Diego-based collaboration between JCVI, NOAA and the Scripps Institution of Oceanography (SIO) to integrate genome-enabled techniques and technologies (i.e., ‘omics) into the California Cooperative Oceanic Fisherines Investigations (CalCOFI). CalCOFI is a multi-partner, long-term ecosystem and fisheries study off the coast of California in it’s 7th decade.

The most recent $2.5 Million gift in 2012 for the completion of the new J. Craig Venter Institute sustainable laboratory was recognized by naming the third floor ocean view conference room and terrace the “Bob and Betty Beyster Conference Room” and the “Bob and Betty Beyster Terrace”.

Left: Looking up at the Beyster Conference Room and Terrace from the ground floor. Right: Sunset on the Beyster Terrace.

Dr. Beyster will be greatly missed by his family, friends and colleagues. We are fortunate to have a constant a reminder of his generosity and support. A link to his obituary can be found here.

On Sunday, December 14th JCVI scientists Andy Allen, Erin Bertrand, and Jeff Hoffman flew to New Zealand to begin the arduous journey to the sea ice edge of Antarctica. The JCVI team was joined by three members of the University of Southern California, led by David Hutchins, and three members of the Virginia Institute of Marine Science (VIMS), led by Deborah Bronk. This is the second field season of the second three-year NSF funded collaborative project for the Allen team. The first field season for the current project was in December 2012/January 2013; the second year was postponed due to the government shutdown in late 2013 delaying our trip until December 2014. The major objectives of this collective fieldwork are to understand how changes in micronutrient availability, temperature, and pCO2 will impact growth, community composition, and nutrient utilization in Southern Ocean phytoplankton.

Pictures from Antarctic Expedition

Antarctica and the Southern Ocean remain one of the most untouched regions on the planet making this area extremely valuable for research related to the impacts of climate change on biota. The Southern Ocean is a system of currents linking all of the Earth’s ocean. It is the most prolific of our oceans, and by conducting genome-enabled investigations targeting phytoplankton, plant like organisms consisting mostly of algae and bacteria that are the base of oceanic food webs, JCVI scientists glean insight into key biological underpinnings. A key research challenge is identification of basic characteristics, features and genomic fingerprints that are sensitive to environmental shifts that impact surface waters and result in nutrient cascading effects. JCVI scientists are establishing valuable baselines to identify impacts of climate change on ocean ecosystems. This research is used in turn to create models of ocean circulation and phytoplankton distribution patterns that will help scientists, policy makers and politicians identify and address the worldwide effects of climate change.

This research can be especially challenging because of the geographic isolation of the Southern Ocean. Upon arrival in New Zealand, the JCVI team spends a day securing extreme cold weather gear and viewing safety videos. We then wait patiently to depart on a military plane: LC-130 Hercules. While the LC-130 is known for its reliability to reach austere locations, the flight is often at the mercy of mechanical failure and weather changes. After a nine hour, extremely loud and rumbling flight, the team disembarks onto a sheet of ice. Despite this being a repeat trip for many of us, it is still amazing to find yourself traversing a remote sheet of ice. From here, we board the transport vehicle Ivan the Terra Bus for the 45-minute ride to McMurdo Station on Ross Island.

Orientation to station life can be challenging. There are acronyms for everything. Despite the presence of approximately 1000 residents, one is aware of the lack of “home like” sounds from pets and children, and the feelings of isolation are real and enduring. Interestingly less than 10% of the Station population is scientists. We work with military and station support staff daily, and despite the isolation, a sense of camaraderie and a bond based on shared experience develops immediately. Another note of interest is that the weather at times is not that bad at McMurdo despite what you may have seen in the movies. In fact, our friends and family in Boston had it much worse!

After arriving at McMurdo, the team spent 9 days completing required safety training, securing logistical support and preparing the lab. Our research activities consisted of weekly helicopter expeditions to the sea ice edge where large volumes of water were filtered for analyses of DNA, RNA and proteins. Live phytoplankton samples were also collected in a manner specifically designed to prevent contamination by iron and other trace metals. There are inherent dangers traveling to the sea ice edge. In the company of penguins and whales, the team must be aware of potential ice shifts, developing cracks and breakouts. We travel with a mountaineer who works to maintain our safety. When working close to the ice edge, we are each secured via ropes and pulleys—it can be intense. We also have to watch the weather. Many times in order to keep samples from freezing, you could see us breaking out the hairdryers and camping stoves. Whatever it takes!

Our “live water” samples were transported back to the laboratory at McMurdo and used to conduct various manipulative experiments aimed at investigating the synergistic impact of change in Iron (Fe) and Vitamin B12 availability as well as increases in temperature and pCO2 levels. One of the major challenges the team faced was keeping these experiments free of dust in order to avoid iron contamination. This was a particular challenge because McMurdo Station is built on a pile of extremely dry, dusty, volcanic soil. The team persevered, of course, and completed numerous trace metal clean experiments.

To date, these manipulative experiments have yielded preliminary results suggesting that changing micronutrient availability and increasing temperature will have major impacts on the base of the Antarctic food web. These include changes in mutualistic relationships between phytoplankton and bacteria and changes in the rate of consumption in major nutrients, both of which are likely to have important downstream effects throughout the global ocean. Analyses of gene and protein expression changes in the field and in these experiments are just beginning to yield further insight into how the Southern Ocean will respond to a changing earth.

On January 27th, exhausted, but with a very successful expedition completed, the team returned to New Zealand. It is challenging to be away from your friends and family for 2 months at time. As we return to the real world though, we arrive feeling lucky and privileged. JCVI scientists see a region of the world and experience amazing days of wildlife that few people will ever know first-hand. Studying phytoplankton and ocean ecosystems is in fact a privilege and the research JCVI scientists and other teams are doing in Antarctica will have a lasting impact on the future of our planet.

Every March, the New Hampton School, an independent high school in New Hampshire, holds Project Week, an experiential learning program that allows students to choose from a wide array of unique activities, both on and off campus. This year, one project group traveled to Washington D.C. to complete a program on forensic biology, which included activities at both the Crime Museum and the J. Craig Venter Institute (JCVI).

On Wednesday, March 11, 2015, ten high school students and two teachers visited JCVI to learn about molecular biology techniques and animal forensics. Their activities were coordinated by Dr. Karla Stucker, a Postdoctoral Fellow in the Virology Group at JCVI, and included a review of DNA structure and replication, a tour of the Institute, lessons about PCR and gel electrophoresis techniques, hands-on laboratory exercises, and a discussion about animal forensics with case examples. Dr. Suchismita Chandran, a Postdoctoral Fellow in the Synthetic Biology Group at JCVI, assisted with the laboratory exercises.

Upon arrival, each participant “adopted” a dog for the day by picking from various photos of different pure-bred and mixed breed dogs. They thus became dog owners living in an upscale apartment complex in Bethesda, where they were required to submit cheek swab samples from their pets to be entered into a DNA database. Our gel electrophoresis experiment was designed to reveal which dog owner(s) failed to pick up after their pet(s) by checking for a match between cheek swab samples and a stool sample. The test made use of size differences in PCR amplicons from a hypothetical microsatellite marker that helps distinguish dog breeds. We also discussed more serious animal forensic cases, including those involving wildlife trafficking and the recent case of a poisoned show dog at Crufts, a large dog show in the UK.

Each day, the students blog about their experiences. One student, Amy, wrote, “We saw many young and passionate researchers working hard in their labs, which made us feel excited and got us looking forward to being scientists. The lab room was clean, organized and bright. We were not allowed to touch anything without gloves due to personal protection. After visiting, we have a better understanding of how scientists’ workplaces should look like, and their rigorous attitudes towards science.”

I was lucky enough to help set up and plan a workshop covering genomics, metagenomics, proteomics and bioinformatics at the University of the West Indies campus in St. Augustine, Trinidad & Tobago on February 19th and 20th. The workshop was sponsored by the National Institute of Allergy and Infectious Diseases through the Genomic Center for Infectious Diseases cooperative agreement. UWI was a co-sponsor and a gracious host. Participants included 60 individuals from Trinidad, England, Guyana and Barbados. On-line participants were from all over the world including Gambia, Ethiopia, Kenya, India, USA, and the Caribbean.

The team of presenters from the JCVI included Karen Nelson, Bill Nierman, Andrey Tovchigrechko, Rembert Pieper, and Shibu Yooseph. Presenters from UWI included Drs. Christine Carrington and Adesh Ramsubhag.

Karen opened the workshop with a welcome message and overview. She has been a driving force behind the growing relationship between UWI and JCVI. Bill delivered very interesting talks on the history of research on the human microbiome and currently emerging infectious diseases. Rembert handled a presentation and tutorial on proteomic analysis strategies, which was a big hit. If time was not a factor, the question and answer period could have lasted longer than his talk. Finally, Andrey and Shibu presented and gave lessons on statistics, UNIX, and bioinformatics analyses for genomics, metagenomics, and microbiome work.

Dr. Ramsubhag described the results of his work examining the bacterial diversity of the Nariva Swamp in Trinidad, which uncovered many unique bacterial strains. Perhaps the most important portion of his talk described how important this type of workshop/collaboration is for UWI. Lessons from subject matter experts are invaluable to the undergraduate, graduate and faculty members that attended the workshop as students. In addition, Dr. Ramsuhbag described how a relationship that started through a workshop has given UWI access to cutting edge technologies and data analysis strategies that would be otherwise unavailable without the collaboration with the JCVI.

The students that attended the workshop were all very enthusiastic and eager to learn. They seemingly hung on every word from the presenters, and paid very close attention during the presentations and hands on informatics sessions. A few attendees even asked us to make the lunch break shorter so that the workshop time could be lengthened…but we needed that time to break down the video equipment, haul it to another building and set it up for the afternoon classes. It was a pleasure to help make this learning experience possible for the workshop students!

The workshop was the second time that staff from the JCVI have presented at the St. Augustine Campus of UWI. Tim Stockwell held an 8 hour workshop focused on viruses in 2013. We look forward to working together in the future.

Special thanks to Tim Stayeas for handling all of the technology associated with on-line broadcasts of the meeting.

20th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology (VEME) on behalf of the International Centre for Genetic Engineering and Biotechnology

The International Bioinformatics Workshop on VEME workshop is recognized as one of the best virus bioinformatics courses in the world and has so far been organized in Belgium, Brazil, Finland, Greece, Portugal, the USA, South Africa, The Netherlands, Serbia and Italy. The 20th edition will be held 9 – 14 August 2015 at the University of the West Indies (UWI) in Trinidad and Tobago. The workshop is co-organized by the UWI, J. Craig Venter Institute (JCVI) and the University of Leuven.

The workshop will provide intensive training in the mathematical principles and computer applications used in the study virus evolution and for conducting detailed molecular epidemiological investigations. The workshop will include lectures and computer practical session where students will have the opportunity to analyze their own research data. Teachers will include 24 world-renowned researchers (including Richard Scheuermann, Tim Stockwell and Karen E. Nelson from JCVI).

Guests experienced our science first hand through various displays and had the opportunity to interact with many JCVI scientists to learn how advances in genomics are impacting our health and environment.

JCVI Scientists Manny Torralba and Stephanie Mounaud welcomed guests with a brief introduction to the palm microbiome by taking swabs and sharing aggregate population results midevening.

Following welcome remarks by J. Craig Venter, Ph.D., Founder & CEO of JCVI, Marlo Gottfurcht Longstreet shared her son Tanner’s battle with a Giloblastoma Brain Tumor. It is understood that the tumor developed as a result of a mutation in the TP53 tumor suppressor gene. Sadly, Tanner Jay Longstreet passed away in 2013 at the age of 11.

Marlo Gottfurcht Longstreet sharing her personal story about her son Tanner and ongoing work at the Tanner Project.

Personal tragedy turned mission for Marlo as she set out to do everything she could to better understand what afflicted Tanner, which gave rise to the Tanner Project at JCVI. Led by Nicholas Schork, Ph.D., the Tanner Project is what is referred to as an “N of 1” project – a single patient case study. Rather than go in for yearly checkups, the patient in the study is monitored daily so that any evidence of cancer can be detected at onset. The goal is to keep the study patient at what is referred to as stage 0. By closely monitoring the condition in this “N of 1” study, its application can be applied more broadly in personalized medicine – “N of 1 for everyone.”

Dr. Ornish discussed advances in personalized medicine and how simple behavioral changes can greatly affect patient outcomes. He addressed ideas presented in his most recent book, The Spectrum, suggesting diet and exercise are not all or nothing propositions. If today wasn’t a great food day, there is no reason tomorrow can’t be. This kind of thinking can greatly improve longevity and quality of life.

JCVI remains committed to tackling today’s pressing medical and environmental concerns, and we continue to rely on your generosity to achieve our goals. For more information on funding needs and opportunities, please contact Katie Collins as kcollins@jcvi.org.

We have all read the stories with concern about the rapid spread of Ebola virus disease (EVD) in Africa. Now, with the first diagnosis of the virus in the United States, it is clear this virus is not under control. If not contained, Ebola poses a significant threat to the African continent and beyond. JCVI is on the front lines of working to better understand this infectious agent. Dr. Reed Shabman, a member of JCVI’s infectious disease team, is seeking to understand why Ebola and Marburg viruses (both are filoviruses) infections result in such severe human disease.

Produced by the National Institute of Allergy and Infectious Diseases (NIAID), under a magnification of 25,000X, this digitally-colorized scanning electron micrograph (SEM) depicts numerous filamentous Ebola virus particles (red) budding from a chronically-infected VERO E6 cell (blue). Image credit: NIAID

During his time as a postdoc at the Icahn School of Medicine at Mount Sinai in New York, Reed helped to develop research platforms designed to understand how Ebola virus mediates its replication, gene expression and evades the immune system. The innovative approaches used at JCVI do not require high level containment facilities and through established collaborations with Biosafety level-4 (BSL-4) labs his group is able to confirm their results in the context of actual Ebola infection.

Developing reporter systems to understand how the untranslated regions (UTRs) of Ebola and Marburg virus control their protein production.

This important research seeks to enhance the scientific community’s understanding of Ebola and Marburg virus biology which will aid in our ability to rationally design ways to combat these deadly viruses.

Ebola Background

Ebola has entered the human population before, with the first documented cases occurring in 1976 in areas that are now South Sudan and the Democratic Republic of Congo. Since 1976, there have been approximately 20 outbreaks in central Africa resulting in just over 2300 confirmed cases of Ebola virus disease (EVD).

One unusual aspect of the current Ebola outbreak is that instead of central Africa, this outbreak is occurring in west Africa. Initial cases were reported in February in Guinea. Shortly after these initial reports, EVD spread into Liberia followed by cases in Sierra Leeone and Nigeria. While efforts to control the virus in Nigeria appear to be successful, the number of cases since the first reported case now totals approximately 8000 with almost 4000 fatalities. The numbers from this single outbreak are larger than all other previous outbreaks combined.

Ebola virus was identified almost 40 years ago; however, there are still no approved vaccines or antiviral approaches beyond supportive care. There are promising therapies and vaccines on the horizon, but a fundamental understanding of how the virus interacts with human host is critical to advance the progress of treating the deadly disease.

Scientists from J. Craig Venter Institute are part of teams awarded grants from NASA to “study the origins, evolution, distribution, and future life in the universe.” Dr. Christopher Dupont is part of a team led by the University of California, Riverside and will study chemical energy stored in rocks as a potential power source, while Dr. Shino Ishii will work with a team from NASA’s Jet Propulsion Laboratory looking at the habitability of extraterrestrial icy worlds.

Artist concept of an early Earth. Image Credit: NASA

From NASA’s Press Release:

NASA’s Jet Propulsion Laboratory, Pasadena, California. Team lead is Isik Kanik. Research will conduct laboratory experiments and field research in environments on Earth, such as The Cedars in Northern California, to understand the habitability of extraterrestrial icy worlds such as Europa, Ganymede and Enceladus.

University of California, Riverside. Team lead is Timothy Lyons. Research will examine the history of oxygen in Earth’s atmosphere and ocean between 3.2 and 0.7 billion years ago. This is a time range in which the amount of oxygen present is thought to have increased from almost nothing to the amounts present today. This work will address the question of how Earth has remained persistently inhabited through most of its dynamic history and would provide NASA exploration scientists a template to investigate the presence of habitable conditions on Mars and other planetary bodies.

Bats species harbor a large number of viruses that cause human disease. So, when the first influenza sequences from Guatemalan little yellow-shouldered bats were uncovered in 2009, the question arose of whether bat influenza viruses pose a threat to human health. A collaborative project between JCVI and Kansas State University was recently published in PLoS Pathogens to address this question.

Image Credit: National Institute of Allergy and Infectious Diseases (NIAID)

The approach employed cutting-edge synthetic biology approaches and demonstrated that, while the sequences of the bat influenza virus of the subtype H17N10 are viable, they are unable to infect human cells. Additional experiments clearly indicated that these bat virus sequences are not able to reassort with other influenza A and B viruses known to infect humans. Therefore, the potential for a pandemic bat influenza entering the human population is extremely unlikely.

David Wentworth, the former Director of Viral Programs at JCVI, was the lead investigator for this study. Additional authors from JCVI include Tim Stockwell, Wei Wang, Xudong Lin, Bin Zhou (now at NYU), and Reed Shabman.

The National Institutes of Health (NIH) and the UK-based Wellcome Trust, in partnership with the African Society of Human Genetics, developed a program to foster genomic and epidemiological research in African scientific institutions. The laboratory and computational infrastructure available to most scientists on the African continent is currently insufficient to keep up with the rapid developments in DNA sequencing technologies and the need to use advanced computationally intensive methods to analyze this data.

Through the H3Africa Consortium, a partnership between NIH and Wellcome Trust, funding has become available to support knowledge development and implementation of genomics-centered research in several African academic institutions. The first scientific paper to come from this effort, Enabeling the Genomic Revolution in Africa, was published in the journal Science in June 2014.

H3Africa Efforts at J. Craig Venter Institute (JCVI)

One of the main initiatives of H3Africa is to foster scientific exchange between US-based partners and their African-based consortium members. JCVI is involved in a number of such partnerships through training and research collaborations.

Tuberculosis Research with Addis Ababa University

Addis Ababa University is the only Ethiopian institution to receive a primary award from NIH under H3Africa. It is based on a collaboration with JCVI. Professor Gobena Ameni of Addis Ababa University and Dr. Rembert Pieper of JCVI developed a proposal on Systems Biology for Molecular Analysis of Tuberculosis in Ethiopia which was initiated earlier this year. The research focuses on genomic variability in M. tuberculosis strains in Ethiopian pastoralist societies and also has an oral microbiome and proteomic biomarker discovery component.

Bioinformatics Training for African Scientists

As part of H3Africa, JCVI is leveraging its recent GCID award, where appropriate, for training of African Scientists. As part of this effort Dr. Andrey Tovchigrechko taught microbiome analysis to graduate students in Ibadan, Nigeria. The workshop was organized by the local H3Africa Bioinformatics Network node. The workshop took place in July, 2014 and comprised of students from Nigeria and other West and Central African countries.

During the three day workshop, Dr. Tovchigrechko taught the students launching and controlling computing instances on Amazon cloud, the basics of Python and R programming, MG-RAST Web interface, MG-RAST R package matR and JCVI-developed R code MGSAT. MG-RAST tutorials were provided by one of its developers Andreas Wilke (ANL).

Dr. Tovchigrechko also gave a talk, along with a dozen other speakers, at a one-day symposium at the University of Ibadan that preceded the workshop and included approximately 200 participants. Special thanks go to Nash Oyekanmi, the organizer and manager of the whole event, for his relentless efforts.

Collaborations with University of Cape Town

Also as part of the H3Africa Consortium, Dr. William Nierman from JCVI and Dr. Mark Nicol from the University of Cape Town, South Africa are in collaboration to study the nasopharyngeal microbiome and respiratory disease in African children. Dr. Nierman’s group has conducted a month long in house microbiome training workshop with students from Dr. Nicol’s group.

The focus of the training was to teach students JCVI’s complete microbiome pipeline (including sample preparation, sequencing generation, and final association analysis). The aim of the training collaboration is to ensure that this complete pipeline can be performed at the University of Cape Town, to help build independent and sustainable capacity in this field within South Africa.